Lsm1 (LSM1 homolog, mRNA degradation associated) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Lsm1 (LSM1 homolog, mRNA degradation associated) Rattus norvegicus
Analyze
Symbol: Lsm1
Name: LSM1 homolog, mRNA degradation associated
RGD ID: 1304967
Description: Enables mRNA binding activity and pre-mRNA binding activity. Predicted to be involved in deadenylation-dependent decapping of nuclear-transcribed mRNA and histone mRNA catabolic process. Predicted to act upstream of or within negative regulation of neuron differentiation and stem cell population maintenance. Located in axon; dendrite; and neuronal cell body. Part of ribonucleoprotein complex. Orthologous to human LSM1 (LSM1 homolog, mRNA degradation associated); PARTICIPATES IN RNA degradation pathway; INTERACTS WITH 2,4-dinitrotoluene; bisphenol A; fipronil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC364624; LSM1 homolog, U6 small nuclear RNA associated; LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae); LSM1 mRNA degradation associated; LSM1, U6 small nuclear RNA associated; U6 snRNA-associated Sm-like protein LSm1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81672,980,075 - 72,991,581 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1672,979,686 - 73,022,396 (-)EnsemblGRCr8
mRatBN7.21666,277,345 - 66,288,852 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1666,277,345 - 66,288,852 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1671,555,983 - 71,567,493 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01674,962,293 - 74,973,803 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01670,202,187 - 70,213,697 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01671,046,475 - 71,057,883 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1671,046,475 - 71,057,883 (-)Ensemblrn6Rnor6.0
Rnor_5.01670,711,151 - 70,722,559 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41670,652,831 - 70,663,995 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1664,187,220 - 64,198,747 (-)NCBICelera
RGSC_v3.11670,653,556 - 70,663,907 (-)NCBI
Cytogenetic Map16q12.4NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
axon  (IDA)
cytoplasm  (IEA,ISO)
dendrite  (IDA)
Lsm1-7-Pat1 complex  (IBA)
neuronal cell body  (IDA)
nucleus  (ISO)
P-body  (IBA,IEA,ISO)
ribonucleoprotein complex  (IDA,IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Dendritic LSm1/CBP80-mRNPs mark the early steps of transport commitment and translational control. di Penta A, etal., J Cell Biol. 2009 Feb 9;184(3):423-35. doi: 10.1083/jcb.200807033. Epub 2009 Feb 2.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:18172165   PMID:18559850   PMID:18719247   PMID:22658674   PMID:22681889   PMID:25456498  


Genomics

Comparative Map Data
Lsm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81672,980,075 - 72,991,581 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1672,979,686 - 73,022,396 (-)EnsemblGRCr8
mRatBN7.21666,277,345 - 66,288,852 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1666,277,345 - 66,288,852 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1671,555,983 - 71,567,493 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01674,962,293 - 74,973,803 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01670,202,187 - 70,213,697 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01671,046,475 - 71,057,883 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1671,046,475 - 71,057,883 (-)Ensemblrn6Rnor6.0
Rnor_5.01670,711,151 - 70,722,559 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41670,652,831 - 70,663,995 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1664,187,220 - 64,198,747 (-)NCBICelera
RGSC_v3.11670,653,556 - 70,663,907 (-)NCBI
Cytogenetic Map16q12.4NCBI
LSM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38838,163,321 - 38,176,730 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl838,163,335 - 38,176,730 (-)Ensemblhg38GRCh38
GRCh37838,020,839 - 38,034,248 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36838,140,014 - 38,153,183 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34838,140,013 - 38,153,183NCBI
Celera836,973,393 - 36,986,562 (-)NCBICelera
Cytogenetic Map8p11.23NCBI
HuRef836,555,756 - 36,568,636 (-)NCBIHuRef
CHM1_1838,222,844 - 38,236,249 (-)NCBICHM1_1
T2T-CHM13v2.0838,440,300 - 38,453,709 (-)NCBIT2T-CHM13v2.0
Lsm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39826,275,326 - 26,294,003 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl826,275,316 - 26,294,003 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38825,785,318 - 25,803,975 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl825,785,288 - 25,803,975 (+)Ensemblmm10GRCm38
MGSCv37826,896,063 - 26,914,447 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36827,250,852 - 27,269,520 (+)NCBIMGSCv36mm8
Celera827,253,809 - 27,272,186 (+)NCBICelera
Cytogenetic Map8A2NCBI
cM Map814.17NCBI
Lsm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546313,773,869 - 13,788,784 (-)Ensembl
ChiLan1.0NW_00495546313,775,639 - 13,788,784 (-)NCBIChiLan1.0ChiLan1.0
LSM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2756,726,906 - 56,739,998 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1832,443,915 - 32,457,154 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0837,465,986 - 37,479,186 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1834,642,938 - 34,656,142 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl834,642,938 - 34,656,142 (-)EnsemblpanPan2panpan1.1
LSM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11627,304,257 - 27,315,389 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1627,304,198 - 27,315,233 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1627,821,271 - 27,832,688 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01629,203,163 - 29,214,621 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1629,203,401 - 29,214,465 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11627,425,471 - 27,436,928 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01628,002,718 - 28,014,129 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01628,041,959 - 28,053,408 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Lsm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494349,909,516 - 49,915,246 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367101,545,790 - 1,552,394 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049367101,546,027 - 1,551,685 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1548,348,648 - 48,365,106 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11548,348,653 - 48,360,004 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21555,604,059 - 55,615,385 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LSM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1836,184,928 - 36,198,689 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl836,182,380 - 36,198,704 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660525,791,244 - 5,805,004 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lsm1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247805,473,041 - 5,483,300 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247805,473,172 - 5,483,584 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Lsm1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11360,697,417 - 60,713,458 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Lsm1
61 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:427
Count of miRNA genes:217
Interacting mature miRNAs:255
Transcripts:ENSRNOT00000020721
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164445512389455123Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)163692878281928782Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)164199206486992064Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162846870173468701Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164909919691442908Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)166241446475736480Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)163236104377361043Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)163105803976058039Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165942871491442908Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)163439829479398294Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)163188527176885271Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164445512389455123Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165942871491442908Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165942871491442908Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000020721   ⟹   ENSRNOP00000020721
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1672,980,075 - 72,991,581 (-)Ensembl
mRatBN7.2 Ensembl1666,277,345 - 66,288,852 (-)Ensembl
Rnor_6.0 Ensembl1671,046,475 - 71,057,883 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000118602   ⟹   ENSRNOP00000089972
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1672,980,075 - 73,007,719 (-)Ensembl
mRatBN7.2 Ensembl1666,277,345 - 66,283,881 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000141067   ⟹   ENSRNOP00000110697
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1672,980,075 - 73,022,396 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000156554   ⟹   ENSRNOP00000109581
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1672,979,686 - 72,991,427 (-)Ensembl
RefSeq Acc Id: NM_001108876   ⟹   NP_001102346
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81672,980,075 - 72,991,581 (-)NCBI
mRatBN7.21666,277,345 - 66,288,852 (-)NCBI
Rnor_6.01671,046,475 - 71,057,883 (-)NCBI
Rnor_5.01670,711,151 - 70,722,559 (-)NCBI
RGSC_v3.41670,652,831 - 70,663,995 (-)RGD
Celera1664,187,220 - 64,198,747 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102346 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM09069 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000020721
  ENSRNOP00000020721.4
  ENSRNOP00000089972.2
  ENSRNOP00000109581.1
  ENSRNOP00000110697.1
RefSeq Acc Id: NP_001102346   ⟸   NM_001108876
- UniProtKB: D3ZWB1 (UniProtKB/TrEMBL),   A6IW03 (UniProtKB/TrEMBL),   A0A8I6GHU0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000020721   ⟸   ENSRNOT00000020721
Ensembl Acc Id: ENSRNOP00000089972   ⟸   ENSRNOT00000118602
Ensembl Acc Id: ENSRNOP00000109581   ⟸   ENSRNOT00000156554
Ensembl Acc Id: ENSRNOP00000110697   ⟸   ENSRNOT00000141067
Protein Domains
Sm

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZWB1-F1-model_v2 AlphaFold D3ZWB1 1-133 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13700166
Promoter ID:EPDNEW_R10690
Type:initiation region
Name:Lsm1_1
Description:LSM1 homolog, mRNA degradation associated
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01671,057,642 - 71,057,702EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304967 AgrOrtholog
BioCyc Gene G2FUF-10976 BioCyc
Ensembl Genes ENSRNOG00000015375 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020721 ENTREZGENE
  ENSRNOT00000020721.7 UniProtKB/TrEMBL
  ENSRNOT00000118602.2 UniProtKB/TrEMBL
  ENSRNOT00000141067.1 UniProtKB/TrEMBL
  ENSRNOT00000156554.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.100 UniProtKB/TrEMBL
InterPro IPR047575 UniProtKB/TrEMBL
  Lsm1 UniProtKB/TrEMBL
  LSM_domain UniProtKB/TrEMBL
  LSM_related_domain UniProtKB/TrEMBL
  PTHR15588 UniProtKB/TrEMBL
KEGG Report rno:364624 UniProtKB/TrEMBL
NCBI Gene 364624 ENTREZGENE
PANTHER PTHR15588 UniProtKB/TrEMBL
  U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM1 UniProtKB/TrEMBL
Pfam LSM UniProtKB/TrEMBL
PhenoGen Lsm1 PhenoGen
PROSITE PS52002 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000015375 RatGTEx
SMART SM00651 UniProtKB/TrEMBL
Superfamily-SCOP Sm_like_riboprot UniProtKB/TrEMBL
UniProt A0A8I6GHU0 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LWE5_RAT UniProtKB/TrEMBL
  A0ABK0M320_RAT UniProtKB/TrEMBL
  A6IW03 ENTREZGENE, UniProtKB/TrEMBL
  D3ZWB1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-09 Lsm1  LSM1 homolog, mRNA degradation associated  Lsm1  LSM1 mRNA degradation associated  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-01 Lsm1  LSM1 mRNA degradation associated  Lsm1  LSM1, U6 small nuclear RNA associated  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-03-07 Lsm1  LSM1, U6 small nuclear RNA associated  Lsm1  LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Lsm1  LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)   Lsm1_predicted  LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Lsm1_predicted  LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) (predicted)      Symbol and Name status set to approved 70820 APPROVED